Workflow: bwa-mem-sort-distr.cwl
Fetched 2023-01-14 09:20:20 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
BSD 2-clause "Simplified" License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| sample | String (Optional) | ||
| library | String (Optional) | ||
| threads | Integer (Optional) | ||
| platform | String (Optional) | ||
| readgroup | String (Optional) | ||
| reference | File | ||
| chunk_size | Integer (Optional) | ||
| input_reads | File[] | ||
| output_file | String | ||
| sort_threads | Integer (Optional) | ||
| extract_chunks | String[] | ||
| mark_secondary | Boolean (Optional) | ||
| sort_reference | File (Optional) | ||
| bam_compression | Integer (Optional) | ||
| min_std_max_min | Integer[] (Optional) | ||
| advanced_options | String[] (Optional) | ||
| minimum_seed_length | Integer (Optional) | ||
| input_reads_index_file | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bwa |
../algo/bwa-mem-sort-with-fastq-slicer.cwl
(CommandLineTool)
|
||
| merge |
../algo/bam-merge.cwl
(CommandLineTool)
|
merge sorted bam files. If input bam files are in the order of coordinate, and no overlap, mergemode 10 can be used |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output | File |
Permalink:
https://w3id.org/cwl/view/git/d20382adfe7285cb517a25d95d2bcb7586546e23/stage/bwa-mem-sort-distr.cwl
